The broad, long term objective of the Stanford Technology Accelerating Medicines Partnership (STAMP) Center is to serve as the leader within the RA/SLE AMP Network in the development and implementation of multiplexed mechanistic assays for AMP studies. Although we propose to focus on SLE, our methods will be used in pilot studies for RA and can be applied to any autoimmune disease. Investigators participating in this AMP proposal, and other collaborators at Stanford, have been leading innovators in the development of high-throughput genomics and proteomics technologies for studying cancer and autoimmunity. Project 1 (Steve Quake and Howard Chang) will perform transcript profiling using RNA-Seq of single cells isolated from tissue samples and blood, then separating into individual wells using Fluidigm-based microfluidics devices (C1) or FACS. The Chang lab will determine binding of transcription factors to open chromatin, repressing and/or activating transcriptional programs involving NFAT, NFB, RORs, IRFs, STATs, and other transcription factors. Project 2 (Garry Nolan) will employ CyTOF to study cells obtained from blood and tissue, characterizing cell surface molecules, signaling molecules, and phospho-specific epitopes in discrete cellular subsets. Upregulated transcripts from Project 1 will inform selection of CyTOF antibodies in an iterative process during the UH3 funding period. Project 3 (Bill Robinson, Mark Davis and PJ Utz) will use autoantibody profiling, FACS, repertoire-sequencing and yeast display to characterize antigen- specific B and T cells in blood and isolated from tissues. The Robinson and Davis labs will characterize the B and T cell receptor repertoire by sequencing heavy and light chain genes from FACS sorted plasmablasts, and FACS or tetramer sorted T cells, as well as cells isolated from tissue. Monoclonal antibodies will be cloned, expressed, and purified for antigen identification. Antigen targets will be discovered (Utz and Robinson) using protein arrays, which will serve as a core assay for all AMP Network Centers. Pilot projects are also proposed including plasma virome sequencing and two projects to develop and implement multiplexed ion beam imaging (MIBI). Finally, to insure availability of blood, kidney, skin, and synovium for our studies, subjects will be recruited from Stanford and the Bay Area (SLE); UCLA and Cedars- Sinai (SLE); and UCSD (RA), as well as from other AMP Centers. Integration of all assays at one AMP Center will facilitate discovery of pathways, molecules, and new drug targets.